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SNARE-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Profilin-like [ 55769] (10)
Superfamily:   SNARE-like [ 64356] (4)
Families:   Synatpobrevin N-terminal domain [ 64357] (2)
  Sedlin (SEDL) [ 82767]
  Clathrin coat assembly domain [ 75521] (2)
  SRP alpha N-terminal domain-like [ 90019] (2)


Superfamily statistics
Genomes (498) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 11,805 12,400 11
Proteins 11,744 12,365 11


Functional annotation
General category General
Detailed category Protein interaction

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)single-organism cellular process0.000022460.00000000000001264Least InformativeDirect
Biological Process (BP)localization00Least InformativeDirect
Biological Process (BP)regulation of cellular process11Least InformativeInherited
Biological Process (BP)regulation of metabolic process0.52181Least InformativeInherited
Biological Process (BP)multicellular organismal process0.66761Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.41310.05716Least InformativeInherited
Biological Process (BP)cellular localization0.0000000000000016880Moderately InformativeDirect
Biological Process (BP)regulation of signal transduction0.21011Moderately InformativeInherited
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.029021Moderately InformativeInherited
Biological Process (BP)regulation of phosphate metabolic process10.9888Moderately InformativeInherited
Biological Process (BP)regulation of catalytic activity0.17871Moderately InformativeInherited
Biological Process (BP)macromolecule localization0.28390.001664Moderately InformativeInherited
Biological Process (BP)organic substance transport10.2352Moderately InformativeInherited
Biological Process (BP)regulation of localization0.38920.5038Moderately InformativeInherited
Biological Process (BP)system process0.11910.002749Moderately InformativeInherited
Biological Process (BP)organelle organization10.3553Moderately InformativeInherited
Biological Process (BP)regulation of biological quality0.60581Moderately InformativeInherited
Biological Process (BP)synaptic transmission0.0006630.0000000005628InformativeDirect
Biological Process (BP)protein transport0.000000000012290InformativeDirect
Biological Process (BP)vesicle-mediated transport0.00000000001120InformativeDirect
Biological Process (BP)regulation of nucleoside metabolic process0.0029180.08871InformativeInherited
Biological Process (BP)regulation of cellular catabolic process0.004780.3693InformativeInherited
Biological Process (BP)regulation of purine nucleotide metabolic process0.0012470.1746InformativeInherited
Biological Process (BP)organelle localization0.71160.4679InformativeInherited
Biological Process (BP)cellular membrane organization0.05460.0000000001831InformativeInherited
Biological Process (BP)secretion by cell0.010550.00000000001449InformativeInherited
Biological Process (BP)cytoplasmic transport11InformativeInherited
Biological Process (BP)regulation of neurotransmitter levels0.000014070.0000002902Highly InformativeDirect
Biological Process (BP)regulation of lipid storage0.0000051630.00000001669Highly InformativeDirect
Biological Process (BP)vesicle organization0.0000067270Highly InformativeDirect
Biological Process (BP)Golgi vesicle transport0.0000000017190Highly InformativeDirect
Biological Process (BP)establishment of synaptic vesicle localization0.0000016381Highly InformativeInherited
Biological Process (BP)regulation of Ras GTPase activity0.0000041450.01049Highly InformativeInherited
Biological Process (BP)neurotransmitter transport0.005080.02602Highly InformativeInherited
Biological Process (BP)signal release0.000011510.8455Highly InformativeInherited
Molecular Function (MF)transporter activity0.043220.1417Moderately InformativeInherited
Molecular Function (MF)protein transporter activity0.000000036260.0000000005746Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.00054340.00000000769Least InformativeDirect
Cellular Component (CC)protein complex0.0000000061780.000000000000001589Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.046630.00981Least InformativeInherited
Cellular Component (CC)membrane0.009590.000000000000003095Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.15610.0000000000001489Least InformativeInherited
Cellular Component (CC)endomembrane system0.000000000020660Moderately InformativeDirect
Cellular Component (CC)organelle membrane0.00000023260Moderately InformativeDirect
Cellular Component (CC)vesicle0.000000017580Moderately InformativeDirect
Cellular Component (CC)plasma membrane11Moderately InformativeInherited
Cellular Component (CC)Golgi apparatus0.000000000031780InformativeDirect
Cellular Component (CC)coated vesicle0.000000010040.00000004352InformativeDirect
Cellular Component (CC)synapse part0.00018740.00001821InformativeDirect
Cellular Component (CC)Golgi-associated vesicle0.000000001890.000000000000003095Highly InformativeDirect
Cellular Component (CC)trans-Golgi network0.00000019320Highly InformativeDirect
Cellular Component (CC)cytoplasmic vesicle membrane0.0000000000026240.00000002488Highly InformativeDirect
Cellular Component (CC)endocytic vesicle11Highly InformativeInherited
Cellular Component (CC)clathrin-coated vesicle11Highly InformativeInherited
Cellular Component (CC)transport vesicle0.0037020.01195Highly InformativeInherited

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) single-organism cellular process 0.00000000000001264 Least Informative Direct
Biological Process (BP) localization 0 Least Informative Direct
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.05716 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) cellular localization 0 Moderately Informative Direct
Biological Process (BP) system process 0.002749 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of phosphate metabolic process 0.9888 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 1 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.001664 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.2352 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.5038 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.3553 Moderately Informative Inherited
Biological Process (BP) immune system process 0.6573 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) synaptic transmission 0.0000000005628 Informative Direct
Biological Process (BP) protein transport 0 Informative Direct
Biological Process (BP) cellular membrane organization 0.0000000001831 Informative Direct
Biological Process (BP) vesicle-mediated transport 0 Informative Direct
Biological Process (BP) secretion by cell 0.00000000001449 Informative Direct
Biological Process (BP) protein localization to organelle 1 Informative Inherited
Biological Process (BP) regulation of nucleoside metabolic process 0.08871 Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 0.3693 Informative Inherited
Biological Process (BP) regulation of purine nucleotide metabolic process 0.1746 Informative Inherited
Biological Process (BP) organelle localization 0.4679 Informative Inherited
Biological Process (BP) cytoplasmic transport 1 Informative Inherited
Biological Process (BP) cellular component movement 0.7965 Informative Inherited
Biological Process (BP) microtubule-based process 0.06738 Informative Inherited
Biological Process (BP) immune effector process 0.03382 Informative Inherited
Biological Process (BP) immune response 0.3053 Informative Inherited
Biological Process (BP) leukocyte activation 0.0292 Informative Inherited
Biological Process (BP) regulation of neurotransmitter levels 0.0000002902 Highly Informative Direct
Biological Process (BP) myeloid leukocyte activation 0.000004291 Highly Informative Direct
Biological Process (BP) leukocyte activation involved in immune response 0.00001753 Highly Informative Direct
Biological Process (BP) leukocyte mediated immunity 0.0002622 Highly Informative Direct
Biological Process (BP) microtubule-based movement 0.00000000897 Highly Informative Direct
Biological Process (BP) regulation of lipid storage 0.00000001669 Highly Informative Direct
Biological Process (BP) vesicle organization 0 Highly Informative Direct
Biological Process (BP) Golgi vesicle transport 0 Highly Informative Direct
Biological Process (BP) organelle fusion 0.000000000008842 Highly Informative Direct
Biological Process (BP) establishment of synaptic vesicle localization 1 Highly Informative Inherited
Biological Process (BP) regulation of Ras GTPase activity 0.01049 Highly Informative Inherited
Biological Process (BP) cytoskeleton-dependent intracellular transport 0.003184 Highly Informative Inherited
Biological Process (BP) neurotransmitter transport 0.02602 Highly Informative Inherited
Biological Process (BP) signal release 0.8455 Highly Informative Inherited
Biological Process (BP) phagocytosis 0.04125 Highly Informative Inherited
Biological Process (BP) membrane fusion 0.003088 Highly Informative Inherited
Biological Process (BP) exocytosis 0.8687 Highly Informative Inherited
Biological Process (BP) post-embryonic development 0.5562 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) transporter activity 0.1417 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring acyl groups 0.003473 Informative Inherited
Molecular Function (MF) protein transporter activity 0.0000000005746 Highly Informative Direct
Cellular Component (CC) membrane 0.000000000000003095 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.00000000769 Least Informative Direct
Cellular Component (CC) protein complex 0.000000000000001589 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.0000000000001489 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.00981 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 0.000000002073 Moderately Informative Direct
Cellular Component (CC) endomembrane system 0 Moderately Informative Direct
Cellular Component (CC) organelle membrane 0 Moderately Informative Direct
Cellular Component (CC) vesicle 0 Moderately Informative Direct
Cellular Component (CC) plasma membrane 1 Moderately Informative Inherited
Cellular Component (CC) endosome 0.000000009195 Informative Direct
Cellular Component (CC) endoplasmic reticulum membrane 0.00008221 Informative Direct
Cellular Component (CC) Golgi apparatus 0 Informative Direct
Cellular Component (CC) coated vesicle 0.00000004352 Informative Direct
Cellular Component (CC) vacuolar part 0.000000003596 Informative Direct
Cellular Component (CC) synapse part 0.00001821 Informative Direct
Cellular Component (CC) lytic vacuole 0.03857 Informative Inherited
Cellular Component (CC) Golgi-associated vesicle 0.000000000000003095 Highly Informative Direct
Cellular Component (CC) trans-Golgi network 0 Highly Informative Direct
Cellular Component (CC) cytoplasmic vesicle membrane 0.00000002488 Highly Informative Direct
Cellular Component (CC) endosomal part 0.00000005886 Highly Informative Direct
Cellular Component (CC) late endosome 0.0585 Highly Informative Inherited
Cellular Component (CC) endocytic vesicle 1 Highly Informative Inherited
Cellular Component (CC) clathrin-coated vesicle 1 Highly Informative Inherited
Cellular Component (CC) transport vesicle 0.01195 Highly Informative Inherited
Cellular Component (CC) lysosome 0.3135 Highly Informative Inherited

Document: GO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0Least InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0.00007376Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.004389Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.2382Least InformativeInherited
Worm Phenotype (WP)larval development variant0.3909Least InformativeInherited
Worm Phenotype (WP)growth variant0.7563Least InformativeInherited
Worm Phenotype (WP)pattern of transgene expression variant0.00003889Moderately InformativeDirect
Worm Phenotype (WP)organ system development variant0.00008275Moderately InformativeDirect
Worm Phenotype (WP)organism segment morphology variant0.008233Moderately InformativeInherited
Worm Phenotype (WP)chemical response variant0.03482Moderately InformativeInherited
Worm Phenotype (WP)cell organization biogenesis variant0.3587Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.7756Moderately InformativeInherited
Worm Phenotype (WP)germline nuclear positioning variant0.000014InformativeDirect
Worm Phenotype (WP)somatic gonad development variant0.0004648InformativeDirect
Worm Phenotype (WP)sick0.0006275InformativeDirect
Worm Phenotype (WP)pigmentation variant0.001572InformativeInherited
Worm Phenotype (WP)body length variant0.001798InformativeInherited
Worm Phenotype (WP)drug resistant0.001841InformativeInherited
Worm Phenotype (WP)body width variant0.002258InformativeInherited
Worm Phenotype (WP)alimentary system development variant0.09497InformativeInherited
Worm Phenotype (WP)gut granule biogenesis reduced0.0000003662Highly InformativeDirect
Worm Phenotype (WP)cell secretion variant0.00006399Highly InformativeDirect
Worm Phenotype (WP)oocyte septum formation variant0.00006742Highly InformativeDirect
Worm Phenotype (WP)clear0.0001193Highly InformativeDirect
Worm Phenotype (WP)aldicarb resistant0.0002594Highly InformativeDirect
Worm Phenotype (WP)molt variant0.0006612Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)intracellular transport0.02675InformativeInherited
Yeast Phenotype (YP)protein transport0.003887Highly InformativeInherited

Document: YP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organ system0Least InformativeDirect

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)pollen tube cell0.00004446InformativeDirect
Plant structure DEvelopment stage (PDE)pollen development stage0.0001194Moderately InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processProtein transport0Moderately InformativeDirect
Biological processEndocytosis0InformativeDirect
Biological processER-Golgi transport0Highly InformativeDirect
Biological processExocytosis0.0000001079Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
Cellular componentGolgi apparatus0Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0Moderately InformativeDirect
Cellular componentEndosome0.000000001593Moderately InformativeDirect
Cellular componentCell junction0.001342Moderately InformativeInherited
Cellular componentLysosome0.000000219InformativeDirect
Cellular componentSynapse0.000001332InformativeDirect
Cellular componentCoated pit0Highly InformativeDirect
Cellular componentSynaptosome0.000006642Highly InformativeDirect
DomainTransmembrane0.000009226Least InformativeDirect
DomainCoiled coil0Moderately InformativeDirect
Molecular functionLipid-binding0.0000009165InformativeDirect
Post-translational modificationAcetylation0.000006509Least InformativeDirect
Post-translational modificationPhosphoprotein0.000009611Least InformativeDirect
Post-translational modificationPalmitate0.0000000000000827Moderately InformativeDirect
Post-translational modificationMethylation0.00000000396Moderately InformativeDirect
Post-translational modificationPrenylation0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011012 SSF64356 Protein matches
Abstract

VAMPs (and its homologue synaptobrevins) define a group of SNARE proteins that contain a C-terminal coiled-coil/SNARE motif, in combination with variable N-terminal domains that are used to classify VAMPs: those containing longin N-terminal domains (~150 aa) are referred to as longins, while those with shorter N-termini are referred to as brevins [PubMed12914952]. Longins are the only type of VAMP protein found in all eukaryotes, suggesting that their longin domain is essential. The longin domain is thought to exert a regulatory function. Longin domains have been shown to share the same structural fold, a profilin-like globular domain consisting of a five-stranded antiparallel beta-sheet that is sandwiched by an alpha-helix on one side, and two alpha-helices on the other (beta(2)-alpha-beta(3)-alpha(2)).

Other families have been shown to contain domains that structurally resemble the VAMP longin domain. An example is the eukaryotic conserved protein, SEDL, which is a component of the transport protein particle (TRAPP), critically involved in endoplasmic reticulum-to-Golgi vesicle transport; mutations in the SEDL gene are associated with an X-linked skeletal disorder, spondyloepiphyseal dysplasia tarda [PubMed12361953]. Another example is the assembly domain of clathrin coat proteins, such as Mu2 adaptin (AP50) and Sigma2 adaptin (AP17), which structurally resemble the longin domain. AP50 and AP17 are two of the proteins that make up the core of AP2, a complex that functions in clathrin-mediated endocytosis [PubMed12086608].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 7 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a SNARE-like domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 7 hidden Markov models representing the SNARE-like superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]